[BioC] why is the CMA package not available for windows??

[Patrick Aboyoun]

Maria,
The reason is because CMA fails to pass check on Windows due to MikTex  
issues when processing the examples in the *.Rd man pages. I spent  
some time during the
  BioC 2.3 release and realized untangling this issue would take  
longer than I had to spend. When BioC 2.4 is ready to release in a  
couple of months, I'll probably spend some time again trying to fix  
CMA so it builds on Windows. If, however, someone has a chance to work  
on this package before then, we can make this package available on  
Windows sooner. This package doesn't require 3rd party libraries or  
code compilation, so in that respects it is easy to work with.


D:\sandbox>D:\biocbld\bbs-2.4-bioc\R\bin\R CMD check CMA_1.1.1.tar.gz
...
* checking examples ... ERROR
Running examples in 'CMA-Ex.R' failed.
The error most likely occurred in:

> ### * ElasticNetCMA
>
> flush(stderr()); flush(stdout())
>
> ### Name: ElasticNetCMA
> ### Title: Classification and variable selection by the ElasticNet
> ### Aliases: ElasticNetCMA
> ### Keywords: multivariate
>
> ### ** Examples
>
> ### load Golub AML/ALL data
> data(golub)
> ### extract class labels
> golubY <- golub[,1]
> ### extract gene expression
> golubX <- as.matrix(golub[,-1])
> ### select learningset
> ratio <- 2/3
> set.seed(111)
> learnind <- sample(length(golubY), size=floor(ratio*length(golubY)))
> ### run ElasticNet - penalized logistic regression (no tuning)
> result <- ElasticNetCMA(X=golubX, y=golubY, learnind=learnind,  
> norm.fraction = 0.2, lambda2=0.01)
Loading required package: survival
Loading required package: splines
> AML/ALL data
Error: unexpected symbol in "AML/ALL data"
Execution halted



Quoting "Ortiz, Maria" <mortiz at ceit.es>:

> Hi!
>
> I was wondering why CMA is not available for Windows.
>
> Thanks,
>
> Maria O.
>
> 	[[alternative HTML version deleted]]
>
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